R Markdown test rmd

---

1 data prep spatial layers

read in some data A and data B. Modify some things, and save as layer 1.

2 data prep other layers

This sources a script that modifies another new layer (tableC) and saves it as table2 and table3, external to the direct Rmd path. It also sources a separate script that reads a previously-saved layer (table 1) and gapfills, saving as table1a.

3 model

sourced script reads in layers 1a, 2, and 3, and does some stuff, and saves the results as layers D and E.

---

4 The next section (below the divider) is the footer, knitted as a child

The code for the R code chunk header looks like this:

{r child = file.path(dir_git, 'src/templates/ohibc_prov_ftr.Rmd')}

Note that it is executed as if it were just part of this main document; it numbers the section (“Provenance”) as a continuation of the numbering, and the variables are evaluated in the environment of the main document.

---

5 Provenance

• Run ID: 24 (17f7dda); run tag: “standard run”
• Run elapsed time: 4.558 seconds; run memory usage: NA MB
• System info: System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
• Session info
  • R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
  • Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
  • Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3

run_id	run_tag	run_date	parent_fn	file_loc	filetype	commit_url	commit_author	commit_date	uncommitted_changes	elapsed_time	memory_use	sys_info	ses_info	base_pkgs	attached_pkgs	rdf_subject	rdf_object	rdf_predicate	run_hash
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/tableA.csv	input	https://github.com/OHI-Science/ohibc/commit/8b48c047ef11e01d13c8b61e83e8edc6cce99cf9	Casey O’Hara ohara@nceas.ucsb.edu	Sat Apr 30 12:01:16 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/tableA.csv	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	prov:used	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/tableA2.csv	input	no version control info found	NA	NA	TRUE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/tableA2.csv	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	prov:used	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/tableB.csv	input	https://github.com/OHI-Science/ohibc/commit/00b6e10615d39b60a92958f7d8887c9e1091af54	Casey O’Hara ohara@nceas.ucsb.edu	Sat Apr 30 10:25:32 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/tableB.csv	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	prov:used	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/table1.csv	output	Previous commit: https://github.com/OHI-Science/ohibc/commit/893b6768bfa73aae999c60b5c61cdfd2e501944e	Casey O’Hara ohara@nceas.ucsb.edu	Fri Nov 13 11:03:56 2015 -0800	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/table1.csv	prov:wasGeneratedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/1_data_prep_sample.R	~/github/ohibc/rmd_testing/tableC.csv	input	https://github.com/OHI-Science/ohibc/commit/00b6e10615d39b60a92958f7d8887c9e1091af54	Casey O’Hara ohara@nceas.ucsb.edu	Sat Apr 30 10:25:32 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/tableC.csv	~/github/ohibc/rmd_testing/1_data_prep_sample.R	prov:used	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/1_data_prep_sample.R	~/github/ohibc/rmd_testing/table3.csv	output	Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 16:14:15 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/1_data_prep_sample.R	~/github/ohibc/rmd_testing/table3.csv	prov:wasGeneratedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/1_data_prep_sample.R	~/github/ohibc/rmd_testing/table2.csv	output	Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 16:14:15 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/1_data_prep_sample.R	~/github/ohibc/rmd_testing/table2.csv	prov:wasGeneratedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/1a_gapfill.R	~/github/ohibc/rmd_testing/table1.csv	input	https://github.com/OHI-Science/ohibc/commit/893b6768bfa73aae999c60b5c61cdfd2e501944e	Casey O’Hara ohara@nceas.ucsb.edu	Fri Nov 13 11:03:56 2015 -0800	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/table1.csv	~/github/ohibc/rmd_testing/1a_gapfill.R	prov:used	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/1a_gapfill.R	~/github/ohibc/rmd_testing/table1a.csv	output	Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 16:14:15 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/1a_gapfill.R	~/github/ohibc/rmd_testing/table1a.csv	prov:wasGeneratedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/1_data_prep_sample.R	~/github/ohibc/rmd_testing/1a_gapfill.R	sourced_script	https://github.com/OHI-Science/ohibc/commit/725220e3bd1b4cc62bf54e26091504ca5aff6b0e	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 17:03:26 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/1_data_prep_sample.R	~/github/ohibc/rmd_testing/1a_gapfill.R	prov:wasExecutedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/1_data_prep_sample.R	sourced_script	https://github.com/OHI-Science/ohibc/commit/c265b263de2b0d301dc5e251417e6447e2d42fde	Casey O’Hara ohara@nceas.ucsb.edu	Thu May 5 12:26:36 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/1_data_prep_sample.R	prov:wasExecutedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/2_model_sample.R	~/github/ohibc/rmd_testing/table1a.csv	input	https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 16:14:15 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/table1a.csv	~/github/ohibc/rmd_testing/2_model_sample.R	prov:used	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/2_model_sample.R	~/github/ohibc/rmd_testing/table2.csv	input	https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 16:14:15 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/table2.csv	~/github/ohibc/rmd_testing/2_model_sample.R	prov:used	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/2_model_sample.R	~/github/ohibc/rmd_testing/table3.csv	input	https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 16:14:15 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/table3.csv	~/github/ohibc/rmd_testing/2_model_sample.R	prov:used	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/2_model_sample.R	~/github/ohibc/rmd_testing/tableD.csv	output	Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 16:14:15 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/2_model_sample.R	~/github/ohibc/rmd_testing/tableD.csv	prov:wasGeneratedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/2_model_sample.R	~/github/ohibc/rmd_testing/tableE.csv	output	Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 16:14:15 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/2_model_sample.R	~/github/ohibc/rmd_testing/tableE.csv	prov:wasGeneratedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/2_model_sample.R	sourced_script	https://github.com/OHI-Science/ohibc/commit/725220e3bd1b4cc62bf54e26091504ca5aff6b0e	Casey O’Hara ohara@nceas.ucsb.edu	Tue May 3 17:03:26 2016 -0700	FALSE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/2_model_sample.R	prov:wasExecutedBy	17f7dda5322432bc18624f3988f80d63290ec7d6
24	standard run	Thu May 5 12:35:55 2016	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	parent_script	https://github.com/OHI-Science/ohibc/commit/c265b263de2b0d301dc5e251417e6447e2d42fde	Casey O’Hara ohara@nceas.ucsb.edu	Thu May 5 12:26:36 2016 -0700	TRUE	4.558	NA	System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.	R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).	Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base	Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	~/github/ohibc/rmd_testing/./0_sample_script.Rmd	prov:wasDerivedFrom	17f7dda5322432bc18624f3988f80d63290ec7d6

Provenance summary for run 24 (17f7dda): standard run (Thu May 5 12:35:55 2016)

file_name	file_dir	filetype	uncomm_chgs	commit_hash
table1.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	893b676
table1a.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
table2.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
table3.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
tableA.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	8b48c04
tableA2.csv	/Users/caseyohara	input	TRUE	NA
tableB.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	00b6e10
tableC.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	00b6e10
table1.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	893b676
table1a.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
table2.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
table3.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
tableD.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
tableE.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
0_sample_script.Rmd	/Users/caseyohara/github/ohibc/rmd_testing/.	parent_script	TRUE	c265b26
1_data_prep_sample.R	/Users/caseyohara/github/ohibc/rmd_testing	sourced_script	FALSE	c265b26
1a_gapfill.R	/Users/caseyohara/github/ohibc/rmd_testing	sourced_script	FALSE	725220e
2_model_sample.R	/Users/caseyohara/github/ohibc/rmd_testing	sourced_script	FALSE	725220e